3D structure for 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol (DB03687)

443199
  -OEChem-12241909153D

58 59  0     1  0  0  0  0  0999 V2000
    1.0041    3.8278    1.1340 P   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5365    2.8827   -1.1877 P   0  0  1  0  0  0  0  0  0  0  0  0
    3.0212   -0.7766    1.3305 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0337    0.3526   -0.5838 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3730   -1.0541   -2.2274 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1912    2.7484    0.9226 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2709    3.1821    0.3784 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0777    2.4043   -1.2022 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7526   -1.4680   -0.5450 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7140   -4.0989   -1.0523 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2279    0.8580   -2.0853 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6135    3.6963    2.6985 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3381    5.2239    0.6943 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4880   -1.5567    2.1236 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5803    4.3630   -1.8386 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4471    1.9415   -1.8193 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7777   -2.4000    0.1979 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5992   -4.4451   -0.3042 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5681   -4.7930    0.4637 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6351    0.6190   -0.4825 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8376   -0.5497   -1.0211 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2610    0.6075    0.9934 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9293   -1.5469    0.1211 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9951    1.3965    1.2998 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6665   -1.9570    0.8988 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7443   -3.6757   -0.4203 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4221   -0.3347    0.0193 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.9156    0.9430   -0.6938 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4443   -2.6813    1.0209 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4112    1.1838   -0.5462 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1210   -0.3167    1.5294 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9256   -0.5631   -0.1770 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4399   -4.0126    0.3605 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4424    1.5582   -1.0065 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7987   -0.2547   -1.2024 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0858    0.9740    1.6152 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8296   -2.1676    0.0399 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1322    1.0045    0.7572 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7651    1.3357    2.3689 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2483   -0.4256   -0.0431 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3771   -0.3260   -2.8719 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6994   -0.9874    1.3708 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4563    1.8172   -0.3121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3144   -2.3427    1.5673 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8348    0.3795   -1.0152 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1170    1.2734    0.5018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6611    0.4882    2.0376 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0534   -0.1974    1.7309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5135    0.2477    0.2654 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1808   -0.6283   -1.2408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2511   -1.5121    0.2638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0338   -1.5571   -1.4712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6568    0.1788   -2.4819 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1749    4.1441    3.3666 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3909   -4.4843    0.9711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6096   -5.7083    0.0287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0095   -2.2589    1.6506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6592    4.4507   -2.8124 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  1  7  1  0  0  0  0
  1 12  1  0  0  0  0
  1 13  2  0  0  0  0
  2  7  1  0  0  0  0
  2  8  1  0  0  0  0
  2 15  1  0  0  0  0
  2 16  2  0  0  0  0
  3 22  1  0  0  0  0
  3 23  1  0  0  0  0
  4 20  1  0  0  0  0
  4 40  1  0  0  0  0
  5 21  1  0  0  0  0
  5 41  1  0  0  0  0
  6 24  1  0  0  0  0
  8 30  1  0  0  0  0
  9 27  1  0  0  0  0
  9 52  1  0  0  0  0
 10 26  2  0  0  0  0
 11 28  1  0  0  0  0
 11 53  1  0  0  0  0
 12 54  1  0  0  0  0
 14 31  1  0  0  0  0
 14 57  1  0  0  0  0
 15 58  1  0  0  0  0
 17 23  1  0  0  0  0
 17 25  1  0  0  0  0
 17 26  1  0  0  0  0
 18 26  1  0  0  0  0
 18 33  2  0  0  0  0
 19 33  1  0  0  0  0
 19 55  1  0  0  0  0
 19 56  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 20 34  1  0  0  0  0
 21 23  1  0  0  0  0
 21 35  1  0  0  0  0
 22 24  1  0  0  0  0
 22 36  1  0  0  0  0
 23 37  1  0  0  0  0
 24 38  1  0  0  0  0
 24 39  1  0  0  0  0
 25 29  2  0  0  0  0
 25 42  1  0  0  0  0
 27 28  1  0  0  0  0
 27 31  1  0  0  0  0
 27 32  1  0  0  0  0
 28 30  1  0  0  0  0
 28 43  1  0  0  0  0
 29 33  1  0  0  0  0
 29 44  1  0  0  0  0
 30 45  1  0  0  0  0
 30 46  1  0  0  0  0
 31 47  1  0  0  0  0
 31 48  1  0  0  0  0
 32 49  1  0  0  0  0
 32 50  1  0  0  0  0
 32 51  1  0  0  0  0
M  END
> <DATABASE_ID>
DB03687

> <DATABASE_NAME>
drugbank

> <ORIGINAL_SOURCE>
PUBCHEM

> <ORIGINAL_SOURCE_URL>
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/YFAUKWZNPVBCFF-XHIBXCGHSA-N/SDF?record_type=3d

> <SMILES>
C[C@](O)(CO)[C@H](O)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(N)=NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H25N3O14P2/c1-14(23,6-18)8(19)5-29-33(26,27)31-32(24,25)28-4-7-10(20)11(21)12(30-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21,23H,4-6H2,1H3,(H,24,25)(H,26,27)(H2,15,16,22)/t7-,8-,10-,11-,12-,14+/m1/s1

> <INCHI_KEY>
YFAUKWZNPVBCFF-XHIBXCGHSA-N

> <FORMULA>
C14H25N3O14P2

> <MOLECULAR_WEIGHT>
521.3075

> <EXACT_MASS>
521.081175547

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
58

> <JCHEM_AVERAGE_NEUTRAL_MICROSPECIES_CHARGE>
-1.9241016735081071

> <JCHEM_AVERAGE_POLARIZABILITY>
44.230883620014964

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({hydroxy[(2R,3S)-2,3,4-trihydroxy-3-methylbutoxy]phosphoryl}oxy)phosphinic acid

> <JCHEM_LOGP>
-3.915385796624603

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NEUTRAL_CHARGE>
-2

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.973492605768817

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8397917285445735

> <JCHEM_PKA_STRONGEST_BASIC>
3.5577873357580536

> <JCHEM_POLAR_SURFACE_AREA>
272.34999999999997

> <JCHEM_REFRACTIVITY>
115.04089999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,5R)-5-(5-fluoro-2,4-dioxo-3H-pyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

Similar Structures

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

3D structure for 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol (DB03687)

Structure for 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol (DB03687)